automatic import of python-scvelo

3 files changed, 241 insertions, 0 deletions

diff --git a/.gitignore b/.gitignore
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--- a/.gitignore
+++ b/.gitignore
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+/scvelo-0.2.5.tar.gz
diff --git a/python-scvelo.spec b/python-scvelo.spec
new file mode 100644
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--- /dev/null
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+%global _empty_manifest_terminate_build 0
+Name:		python-scvelo
+Version:	0.2.5
+Release:	1
+Summary:	RNA velocity generalized through dynamical modeling
+License:	BSD
+URL:		https://github.com/theislab/scvelo
+Source0:	https://mirrors.nju.edu.cn/pypi/web/packages/d7/ca/6669ad5c6765493ea9db0fb54b766d043b09db5a146f178c106b7162d1ef/scvelo-0.2.5.tar.gz
+BuildArch:	noarch
+
+Requires:	python3-typing-extensions
+Requires:	python3-anndata
+Requires:	python3-scanpy
+Requires:	python3-loompy
+Requires:	python3-umap-learn
+Requires:	python3-numba
+Requires:	python3-numpy
+Requires:	python3-scipy
+Requires:	python3-pandas
+Requires:	python3-scikit-learn
+Requires:	python3-matplotlib
+Requires:	python3-black
+Requires:	python3-hnswlib
+Requires:	python3-hypothesis
+Requires:	python3-flake8
+Requires:	python3-isort
+Requires:	python3-louvain
+Requires:	python3-magic-impute
+Requires:	python3-pre-commit
+Requires:	python3-pybind11
+Requires:	python3-pytest
+Requires:	python3-pytest-cov
+Requires:	python3-igraph
+Requires:	python3-scanpy
+Requires:	python3-setuptools
+Requires:	python3-setuptools-scm
+Requires:	python3-typing-extensions
+Requires:	python3-importlib-metadata
+Requires:	python3-sphinx-rtd-theme
+Requires:	python3-sphinx-autodoc-typehints
+Requires:	python3-Jinja2
+Requires:	python3-ipykernel
+Requires:	python3-sphinx
+Requires:	python3-nbsphinx
+Requires:	python3-pybind11
+Requires:	python3-hnswlib
+Requires:	python3-igraph
+Requires:	python3-louvain
+
+%description
+**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
+`Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>`_.
+RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
+scVelo generalizes the concept of RNA velocity
+(`La Manno et al., Nature, 2018 <https://doi.org/10.1038/s41586-018-0414-6>`_)
+by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
+transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
+scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
+scVelo's key applications
+^^^^^^^^^^^^^^^^^^^^^^^^^
+- estimate RNA velocity to study cellular dynamics.
+- identify putative driver genes and regimes of regulatory changes.
+- infer a latent time to reconstruct the temporal sequence of transcriptomic events.
+- estimate reaction rates of transcription, splicing and degradation.
+- use statistical tests, e.g., to detect different kinetics regimes.
+scVelo has, for instance, recently been used to study immune response in COVID-19
+patients and dynamic processes in human lung regeneration. Find out more in this list of
+`application examples <https://scholar.google.com/scholar?cites=18195185735875895912>`_.
+Latest news
+^^^^^^^^^^^
+- Aug/2021: `Perspectives paper out in MSB <https://doi.org/10.15252/msb.202110282>`_
+- Feb/2021: scVelo goes multi-core
+- Dec/2020: Cover of `Nature Biotechnology <https://www.nature.com/nbt/volumes/38>`_
+- Nov/2020: Talk at `Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>`_
+- Oct/2020: `Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>`_
+- Oct/2020: Map cell fates with `CellRank <https://cellrank.org>`_
+- Sep/2020: Talk at `Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>`_
+- Aug/2020: `scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>`_
+References
+^^^^^^^^^^
+La Manno *et al.* (2018), RNA velocity of single cells, `Nature <https://doi.org/10.1038/s41586-018-0414-6>`_.
+Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling,
+`Nature Biotech <https://doi.org/10.1038/s41587-020-0591-3>`_.
+Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives,
+`Molecular Systems Biology <https://doi.org/10.15252/msb.202110282>`_.
+Support
+^^^^^^^
+Found a bug or would like to see a feature implemented? Feel free to submit an
+`issue <https://github.com/theislab/scvelo/issues/new/choose>`_.
+Have a question or would like to start a new discussion? Head over to
+`GitHub discussions <https://github.com/theislab/scvelo/discussions>`_.
+In either case, you can also always send us an `email <mailto:mail@scvelo.org>`_.
+Your help to improve scVelo is highly appreciated.
+For further information visit `scvelo.org <https://scvelo.org>`_.
+
+%package -n python3-scvelo
+Summary:	RNA velocity generalized through dynamical modeling
+Provides:	python-scvelo
+BuildRequires:	python3-devel
+BuildRequires:	python3-setuptools
+BuildRequires:	python3-pip
+%description -n python3-scvelo
+**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
+`Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>`_.
+RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
+scVelo generalizes the concept of RNA velocity
+(`La Manno et al., Nature, 2018 <https://doi.org/10.1038/s41586-018-0414-6>`_)
+by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
+transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
+scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
+scVelo's key applications
+^^^^^^^^^^^^^^^^^^^^^^^^^
+- estimate RNA velocity to study cellular dynamics.
+- identify putative driver genes and regimes of regulatory changes.
+- infer a latent time to reconstruct the temporal sequence of transcriptomic events.
+- estimate reaction rates of transcription, splicing and degradation.
+- use statistical tests, e.g., to detect different kinetics regimes.
+scVelo has, for instance, recently been used to study immune response in COVID-19
+patients and dynamic processes in human lung regeneration. Find out more in this list of
+`application examples <https://scholar.google.com/scholar?cites=18195185735875895912>`_.
+Latest news
+^^^^^^^^^^^
+- Aug/2021: `Perspectives paper out in MSB <https://doi.org/10.15252/msb.202110282>`_
+- Feb/2021: scVelo goes multi-core
+- Dec/2020: Cover of `Nature Biotechnology <https://www.nature.com/nbt/volumes/38>`_
+- Nov/2020: Talk at `Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>`_
+- Oct/2020: `Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>`_
+- Oct/2020: Map cell fates with `CellRank <https://cellrank.org>`_
+- Sep/2020: Talk at `Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>`_
+- Aug/2020: `scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>`_
+References
+^^^^^^^^^^
+La Manno *et al.* (2018), RNA velocity of single cells, `Nature <https://doi.org/10.1038/s41586-018-0414-6>`_.
+Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling,
+`Nature Biotech <https://doi.org/10.1038/s41587-020-0591-3>`_.
+Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives,
+`Molecular Systems Biology <https://doi.org/10.15252/msb.202110282>`_.
+Support
+^^^^^^^
+Found a bug or would like to see a feature implemented? Feel free to submit an
+`issue <https://github.com/theislab/scvelo/issues/new/choose>`_.
+Have a question or would like to start a new discussion? Head over to
+`GitHub discussions <https://github.com/theislab/scvelo/discussions>`_.
+In either case, you can also always send us an `email <mailto:mail@scvelo.org>`_.
+Your help to improve scVelo is highly appreciated.
+For further information visit `scvelo.org <https://scvelo.org>`_.
+
+%package help
+Summary:	Development documents and examples for scvelo
+Provides:	python3-scvelo-doc
+%description help
+**scVelo** is a scalable toolkit for RNA velocity analysis in single cells, based on
+`Bergen et al. (Nature Biotech, 2020) <https://doi.org/10.1038/s41587-020-0591-3>`_.
+RNA velocity enables the recovery of directed dynamic information by leveraging splicing kinetics.
+scVelo generalizes the concept of RNA velocity
+(`La Manno et al., Nature, 2018 <https://doi.org/10.1038/s41586-018-0414-6>`_)
+by relaxing previously made assumptions with a stochastic and a dynamical model that solves the full
+transcriptional dynamics. It thereby adapts RNA velocity to widely varying specifications such as non-stationary populations.
+scVelo is compatible with scanpy_ and hosts efficient implementations of all RNA velocity models.
+scVelo's key applications
+^^^^^^^^^^^^^^^^^^^^^^^^^
+- estimate RNA velocity to study cellular dynamics.
+- identify putative driver genes and regimes of regulatory changes.
+- infer a latent time to reconstruct the temporal sequence of transcriptomic events.
+- estimate reaction rates of transcription, splicing and degradation.
+- use statistical tests, e.g., to detect different kinetics regimes.
+scVelo has, for instance, recently been used to study immune response in COVID-19
+patients and dynamic processes in human lung regeneration. Find out more in this list of
+`application examples <https://scholar.google.com/scholar?cites=18195185735875895912>`_.
+Latest news
+^^^^^^^^^^^
+- Aug/2021: `Perspectives paper out in MSB <https://doi.org/10.15252/msb.202110282>`_
+- Feb/2021: scVelo goes multi-core
+- Dec/2020: Cover of `Nature Biotechnology <https://www.nature.com/nbt/volumes/38>`_
+- Nov/2020: Talk at `Single Cell Biology <https://coursesandconferences.wellcomegenomecampus.org/our-events/single-cell-biology-2020/>`_
+- Oct/2020: `Helmholtz Best Paper Award <https://twitter.com/ICBmunich/status/1318611467722199041>`_
+- Oct/2020: Map cell fates with `CellRank <https://cellrank.org>`_
+- Sep/2020: Talk at `Single Cell Omics <https://twitter.com/fabian_theis/status/1305621028056465412>`_
+- Aug/2020: `scVelo out in Nature Biotech <https://www.helmholtz-muenchen.de/en/aktuelles/latest-news/press-information-news/article/48658/index.html>`_
+References
+^^^^^^^^^^
+La Manno *et al.* (2018), RNA velocity of single cells, `Nature <https://doi.org/10.1038/s41586-018-0414-6>`_.
+Bergen *et al.* (2020), Generalizing RNA velocity to transient cell states through dynamical modeling,
+`Nature Biotech <https://doi.org/10.1038/s41587-020-0591-3>`_.
+Bergen *et al.* (2021), RNA velocity - current challenges and future perspectives,
+`Molecular Systems Biology <https://doi.org/10.15252/msb.202110282>`_.
+Support
+^^^^^^^
+Found a bug or would like to see a feature implemented? Feel free to submit an
+`issue <https://github.com/theislab/scvelo/issues/new/choose>`_.
+Have a question or would like to start a new discussion? Head over to
+`GitHub discussions <https://github.com/theislab/scvelo/discussions>`_.
+In either case, you can also always send us an `email <mailto:mail@scvelo.org>`_.
+Your help to improve scVelo is highly appreciated.
+For further information visit `scvelo.org <https://scvelo.org>`_.
+
+%prep
+%autosetup -n scvelo-0.2.5
+
+%build
+%py3_build
+
+%install
+%py3_install
+install -d -m755 %{buildroot}/%{_pkgdocdir}
+if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
+if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
+if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
+if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
+pushd %{buildroot}
+if [ -d usr/lib ]; then
+	find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/lib64 ]; then
+	find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/bin ]; then
+	find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+if [ -d usr/sbin ]; then
+	find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
+fi
+touch doclist.lst
+if [ -d usr/share/man ]; then
+	find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
+fi
+popd
+mv %{buildroot}/filelist.lst .
+mv %{buildroot}/doclist.lst .
+
+%files -n python3-scvelo -f filelist.lst
+%dir %{python3_sitelib}/*
+
+%files help -f doclist.lst
+%{_docdir}/*
+
+%changelog
+* Mon May 15 2023 Python_Bot <Python_Bot@openeuler.org> - 0.2.5-1
+- Package Spec generated
diff --git a/sources b/sources
new file mode 100644
index 0000000..cd94e77
--- /dev/null
+++ b/sources
@@ -0,0 +1 @@
+0d98dbad1515d8aa463e0386cb2d9de0  scvelo-0.2.5.tar.gz